This directory contains a dump of the UCSC genome annotation database for
the Mar. 2011 (Broad/otoGar3) assembly of the bushbaby genome (otoGar3, Broad Institute (GCA_000181295.3)).
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/451
http://www.ncbi.nlm.nih.gov/genome/assembly/249878
http://www.ncbi.nlm.nih.gov/bioproject/16955
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=otoGar3
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/otoGar3/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql otoGar3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql otoGar3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Bushbaby sequence is made freely available before scientific publication
with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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All the files and tables in this directory are freely usable for any purpose.
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Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-20 00:19 43M
xenoRefSeqAli.sql 2020-08-20 00:19 2.1K
xenoRefGene.txt.gz 2020-08-20 00:19 43M
xenoRefGene.sql 2020-08-20 00:19 2.0K
xenoRefFlat.txt.gz 2020-08-20 00:19 39M
xenoRefFlat.sql 2020-08-20 00:19 1.7K
xenoMrna.txt.gz 2020-08-20 00:12 448M
xenoMrna.sql 2020-08-20 00:12 2.1K
windowmaskerSdust.txt.gz 2012-11-21 16:00 124M
windowmaskerSdust.sql 2012-11-21 16:00 1.5K
ucscToRefSeq.txt.gz 2018-02-18 07:56 48K
ucscToRefSeq.sql 2018-02-18 07:56 1.4K
ucscToINSDC.txt.gz 2013-09-15 17:34 49K
ucscToINSDC.sql 2013-09-15 17:34 1.4K
trackDb.txt.gz 2024-01-31 15:13 45K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-24 03:32 3.3K
tableList.sql 2024-11-24 03:32 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 6.4K
tableDescriptions.sql 2024-11-23 02:03 1.5K
simpleRepeat.txt.gz 2012-11-21 15:59 13M
simpleRepeat.sql 2012-11-21 15:59 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 577K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
rmsk.txt.gz 2012-11-21 15:57 111M
rmsk.sql 2012-11-21 15:57 1.9K
netTarSyr2.txt.gz 2015-05-25 07:23 64M
netTarSyr2.sql 2015-05-25 07:23 2.1K
netMm39.txt.gz 2020-11-24 17:51 59M
netMm39.sql 2020-11-24 17:51 2.1K
netMm10.txt.gz 2012-11-21 16:00 59M
netMm10.sql 2012-11-21 15:59 2.1K
netHg38.txt.gz 2018-01-07 09:52 60M
netHg38.sql 2018-01-07 09:52 2.1K
nestedRepeats.txt.gz 2012-11-21 15:57 12M
nestedRepeats.sql 2012-11-21 15:57 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.9M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.5M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.2M
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.1M
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 1.7K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 219K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.5M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
mrnaOrientInfo.txt.gz 2017-07-09 12:09 137
mrnaOrientInfo.sql 2017-07-09 12:09 1.8K
microsat.txt.gz 2015-08-23 23:03 84K
microsat.sql 2015-08-23 23:03 1.5K
history.txt.gz 2012-11-21 16:07 568
history.sql 2012-11-21 16:07 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.3K
gold.txt.gz 2012-11-21 16:07 3.3M
gold.sql 2012-11-21 16:07 1.7K
genscan.txt.gz 2012-11-21 16:07 3.0M
genscan.sql 2012-11-21 16:07 1.7K
gc5BaseBw.txt.gz 2012-11-21 16:07 63
gc5BaseBw.sql 2012-11-21 16:07 1.3K
gbLoaded.txt.gz 2020-08-20 00:19 15K
gbLoaded.sql 2020-08-20 00:19 1.6K
gap.txt.gz 2012-11-21 15:56 2.6M
gap.sql 2012-11-21 15:56 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:40 142K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 86K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensPep.txt.gz 2021-05-25 14:41 6.2M
ensPep.sql 2021-05-25 14:41 1.3K
ensGtp.txt.gz 2021-05-25 14:40 278K
ensGtp.sql 2021-05-25 14:40 1.4K
ensGene.txt.gz 2021-05-25 14:40 2.1M
ensGene.sql 2021-05-25 14:40 1.9K
cytoBandIdeo.txt.gz 2013-04-28 19:52 29K
cytoBandIdeo.sql 2013-04-28 19:52 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:53 482K
cpgIslandExtUnmasked.sql 2014-06-01 17:53 1.7K
cpgIslandExt.txt.gz 2012-11-21 15:59 463K
cpgIslandExt.sql 2012-11-21 15:59 1.7K
chromInfo.txt.gz 2012-11-21 15:56 33K
chromInfo.sql 2012-11-21 15:56 1.4K
chromAlias.txt.gz 2018-02-18 07:56 73K
chromAlias.sql 2018-02-18 07:56 1.4K
chainTarSyr2Link.txt.gz 2015-05-25 06:57 7.0G
chainTarSyr2Link.sql 2015-05-25 06:47 1.5K
chainTarSyr2.txt.gz 2015-05-25 06:37 3.0G
chainTarSyr2.sql 2015-05-25 06:34 1.7K
chainMm39Link.txt.gz 2020-11-24 17:48 426M
chainMm39Link.sql 2020-11-24 17:48 1.6K
chainMm39.txt.gz 2020-11-24 17:45 49M
chainMm39.sql 2020-11-24 17:45 1.7K
chainMm10Link.txt.gz 2012-11-21 16:02 480M
chainMm10Link.sql 2012-11-21 16:01 1.5K
chainMm10.txt.gz 2012-11-21 16:00 65M
chainMm10.sql 2012-11-21 16:00 1.7K
chainHg38Link.txt.gz 2018-01-07 09:49 867M
chainHg38Link.sql 2018-01-07 09:48 1.5K
chainHg38.txt.gz 2018-01-07 09:47 194M
chainHg38.sql 2018-01-07 09:47 1.7K
bigFiles.txt.gz 2024-11-24 03:32 94
bigFiles.sql 2024-11-24 03:32 1.4K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
augustusGene.sql 2015-07-26 17:21 1.9K
all_mrna.txt.gz 2017-07-09 12:08 261
all_mrna.sql 2017-07-09 12:08 2.1K